Skip to content

Add support for charge atom style #269

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 2 commits into from
Nov 20, 2025
Merged

Add support for charge atom style #269

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ff6ee27
Add support for charge atom style
jan-janssen Nov 20, 2025
6c1b627
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 20, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
52 changes: 50 additions & 2 deletions pyiron_lammps/structure.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,12 @@ class LammpsStructure:
input_file_name:
"""

def __init__(self, bond_dict: Optional[Dict] = None, units: str = "metal"):
def __init__(
self,
bond_dict: Optional[Dict] = None,
units: str = "metal",
atom_type: str = "atomic",
):
self._string_input: str = ""
self._structure: Optional[Atoms] = None
self._potential: Optional[Any] = None
Expand All @@ -209,6 +214,7 @@ def __init__(self, bond_dict: Optional[Dict] = None, units: str = "metal"):
self._bond_dict: Optional[Dict] = bond_dict
self._force_skewed: bool = False
self._units: str = units
self._atom_type: str = atom_type

@property
def potential(self) -> Any:
Expand Down Expand Up @@ -238,7 +244,10 @@ def structure(self, structure: Atoms):

"""
self._structure = structure
input_str = self.structure_atomic()
if self._atom_type == "charge":
input_str = self.structure_charge()
else: # self.atom_type == 'atomic'
input_str = self.structure_atomic()
self._string_input = input_str + self._get_velocities_input_string()

def _get_velocities_input_string(self) -> str:
Expand Down Expand Up @@ -382,6 +391,45 @@ def structure_atomic(self) -> str:
+ "\n"
)

def structure_charge(self):
"""
Create atom structure including the atom charges.

By convention the LAMMPS atom type numbers are chose alphabetically for the chemical species.

Returns: LAMMPS readable structure.

"""
species_lammps_id_dict = self.get_lammps_id_dict(self.el_eam_lst)
atoms = "Atoms\n\n"
coords = self.rotate_positions(self._structure)
el_charge_lst = self._structure.get_initial_charges()
el_lst = self._structure.get_chemical_symbols()
for id_atom, (el, coord) in enumerate(zip(el_lst, coords)):
dim = self._structure.positions.shape[1]
c = np.zeros(3)
c[:dim] = coord
atoms += (
"{0:d} {1:d} {2:f} {3:.15f} {4:.15f} {5:.15f}".format(
id_atom + 1,
species_lammps_id_dict[el],
el_charge_lst[id_atom],
c[0],
c[1],
c[2],
)
+ "\n"
)
return (
self.lammps_header(
structure=self.structure,
cell_dimensions=self.simulation_cell(),
species_lammps_id_dict=species_lammps_id_dict,
)
+ atoms
+ "\n"
)
Comment on lines +394 to +431
Copy link
Copy Markdown

@coderabbitai coderabbitai bot Nov 20, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ Potential issue | 🔴 Critical

Missing structure validation check.

Unlike structure_atomic() (lines 367-368), this method doesn't check if self._structure is None before accessing it, which could cause an AttributeError.

Apply this diff to add the validation:

 def structure_charge(self):
     """
     Create atom structure including the atom charges.

     By convention the LAMMPS atom type numbers are chose alphabetically for the chemical species.

     Returns: LAMMPS readable structure.

     """
+    if self._structure is None:
+        raise ValueError("Structure not set")
     species_lammps_id_dict = self.get_lammps_id_dict(self.el_eam_lst)
🤖 Prompt for AI Agents 
In pyiron_lammps/structure.py around lines 394 to 431, add the same validation
present in structure_atomic (around lines 367-368): check if self._structure is
None at the start of structure_charge and raise a clear exception (or otherwise
handle the missing structure) before any access to self._structure to prevent
AttributeError; ensure the new check mirrors the project’s existing error
type/message used in structure_atomic.


def rotate_positions(self, structure: Atoms) -> List[Tuple[float, float, float]]:
"""
Rotate all atomic positions in given structure according to new Prism cell
Expand Down
29 changes: 29 additions & 0 deletions tests/test_structure.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -226,3 +226,32 @@ def test_skewed_cell(self):
cell[0, 1] = cell[0, 0] * 0.6
up = UnfoldingPrism(cell=cell)
self.assertFalse(np.all(np.isclose(up.A, cell)))

def test_structure_charge(self):
atoms = Atoms("Fe1", positions=np.zeros((1, 3)), cell=np.eye(3))
atoms.set_initial_charges(charges=np.ones(len(atoms)) * 2.0)
lmp_structure = LammpsStructure(atom_type="charge")
lmp_structure._el_eam_lst = ["Fe"]
lmp_structure.structure = atoms
self.assertEqual(
lmp_structure._string_input.split("\n"),
[
"Start File for LAMMPS ",
"1 atoms ",
"1 atom types ",
"",
"0. 1.000000000000000 xlo xhi",
"0. 1.000000000000000 ylo yhi",
"0. 1.000000000000000 zlo zhi",
"",
"Masses",
"",
" 1 55.845000 # (Fe) ",
"",
"Atoms",
"",
"1 1 2.000000 0.000000000000000 0.000000000000000 0.000000000000000",
"",
"",
],
)
Loading